P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-12 00:22:34 +02:00
Code Releases Activity

(v1.3.0.9014) as.mo() speed improvement

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-09-03 12:31:48 +02:00
parent 18e52f2725
commit c4b87fe241
93 changed files with 739 additions and 609 deletions
Download Patch File Download Diff File Expand all files Collapse all files

15
man/as.mo.Rd
View File

@ -7,7 +7,7 @@
\alias{mo_failures}
\alias{mo_uncertainties}
\alias{mo_renamed}
\title{Transform to microorganism ID}
\title{Transform input to a microorganism ID}
\usage{
as.mo(
x,
@ -15,6 +15,7 @@ as.mo(
Lancefield = FALSE,
allow_uncertain = TRUE,
reference_df = get_mo_source(),
ignore_pattern = getOption("AMR_ignore_pattern"),
...
)
@ -41,6 +42,8 @@ This excludes \emph{Enterococci} at default (who are in group D), use \code{Lanc
\item{reference_df}{a \code{\link{data.frame}} to be used for extra reference when translating \code{x} to a valid \code{\link{mo}}. See \code{\link[=set_mo_source]{set_mo_source()}} and \code{\link[=get_mo_source]{get_mo_source()}} to automate the usage of your own codes (e.g. used in your analysis or organisation).}
\item{ignore_pattern}{a regular expression (case-insensitive) of which all matches in \code{x} must return \code{NA}. This can be convenient to exclude known non-relevant input and can also be set with the option \code{AMR_ignore_pattern}, e.g. \code{options(AMR_ignore_pattern = "(not reported|contaminated flora)")}.}
\item{...}{other parameters passed on to functions}
}
\value{
@ -52,17 +55,17 @@ Use this function to determine a valid microorganism ID (\code{\link{mo}}). Dete
\details{
\subsection{General info}{
A microorganism ID from this package (class: \code{\link{mo}}) typically looks like these examples:\preformatted{ Code Full name
A microorganism ID from this package (class: \code{\link{mo}}) is human readable and typically looks like these examples:\preformatted{ Code Full name
--------------- --------------------------------------
B_KLBSL Klebsiella
B_KLBSL_PNMN Klebsiella pneumoniae
B_KLBSL_PNMN_RHNS Klebsiella pneumoniae rhinoscleromatis
| | | |
| | | |
| | | ---> subspecies, a 4-5 letter acronym
| | ----> species, a 4-5 letter acronym
| ----> genus, a 5-7 letter acronym
----> taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),
| | | \\---> subspecies, a 4-5 letter acronym
| | \\----> species, a 4-5 letter acronym
| \\----> genus, a 5-7 letter acronym
\\----> taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),
C (Chromista), F (Fungi), P (Protozoa)
}